I assume that you mean that there are titles in the library that aren't in the database? I have never had this problem and have no idea what the "description" you mention says, so the following is a guess:
One way to handle this could be to create a new library and copy all books over to the new library and delete them in the old. All this obviously done in the calibre GUI.
After this the new library should be error free.
Any books left behind in the old library you would have to examine to decide what to do with them. If you have a copy of the same book in the new library, then you can delete the extra left behind copy. Otherwise you'd most likely want to add the book to the new library.
It should be possible to do the same decisions and manipulations directly in the old library, without first creating a new library. But extreme care should be observed to avoid making matters worse.
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